rs2021808

Variant names:

• chr7-128229638-G-A
• rs2021808
• ENST00000690022.1:n.243+6620C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-128229638-G-A
• chr7-128229638-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000690022.1(ENSG00000289434):​n.243+6620C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,278 control chromosomes in the GnomAD database, including 52,663 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.81 (52663 hom., cov: 34)
• Consequence: ENSG00000289434 ENST00000690022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

ENSG00000289434 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289434	ENST00000690022.1	n.243+6620C>T		intron_variant	Intron 2 of 2
ENSG00000289434	ENST00000692614.2	n.519+6620C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122943 AN: 152162 Hom.: 52637 Cov.: 34

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.838

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.808 AC: 123020 AN: 152278 Hom.: 52663 Cov.: 34 AF XY: 0.813 AC XY: 60566 AN XY: 74474

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.941

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.932

Gnomad4 OTH AF: 0.839

Alfa AF: 0.916 Hom.: 83037

Bravo AF: 0.792

Asia WGS AF: 0.907 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.37
DANN	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2021808; hg19: chr7-127869691;